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Inhibitors of herbicidal target IspD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YC3 PDB ENTRY 2YC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 NATIVE CRYSTALS (SEE REMARK 1, PDB 1W77) WERE SOAKED WITH A SATURATED SOLUTION OF LIGAND
Crystal Properties Matthews coefficient Solvent content 2.41 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.06 α = 90 b = 75.06 β = 90 c = 220.82 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARRESEARCH 2006-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 36.5 99.8 0.13 10.84 6.9 22629 -3 38.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 1.36 2.43 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YC3 1.8 73.61 21497 1132 99.79 0.19887 0.197 0.23252 0.2411 RANDOM 30.227
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.49 -0.24 -0.49 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.227 r_dihedral_angle_4_deg 16.879 r_dihedral_angle_3_deg 16.425 r_scangle_it 7.062 r_dihedral_angle_1_deg 6.901 r_scbond_it 4.654 r_mcangle_it 3.124 r_rigid_bond_restr 2.028 r_angle_refined_deg 1.908 r_mcbond_it 1.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.227 r_dihedral_angle_4_deg 16.879 r_dihedral_angle_3_deg 16.425 r_scangle_it 7.062 r_dihedral_angle_1_deg 6.901 r_scbond_it 4.654 r_mcangle_it 3.124 r_rigid_bond_restr 2.028 r_angle_refined_deg 1.908 r_mcbond_it 1.903 r_angle_other_deg 1.035 r_mcbond_other 0.57 r_chiral_restr 0.112 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing